Contacts of the strand formed by residues 22 - 27 (chain B) in PDB entry 4NL3
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 22 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B LYS 3.5 2.0 + - - -
21B ILE* 1.3 78.8 - - - +
23B ALA* 1.3 64.4 + - - +
34B ARG* 3.5 36.3 - - + +
35B GLY* 3.6 14.8 - - - +
36B ARG* 3.7 35.4 - - + +
67B GLN* 2.7 59.1 + - + +
68B LYS* 6.1 0.4 - - - +
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Residues in contact with ALA 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B LEU* 4.5 9.9 - - + -
21B ILE 3.8 3.1 + - - +
22B LEU* 1.3 76.4 - - - +
24B THR* 1.3 62.8 + - - +
25B VAL* 3.8 4.0 + - + +
33B LEU 3.8 0.7 - - - +
34B ARG* 3.4 5.9 - - - +
35B GLY 2.9 38.5 + - - +
36B ARG* 6.0 0.2 - - - -
37B VAL* 5.8 2.9 - - + -
64B PHE* 4.4 22.9 - - + -
65B SER 3.4 12.6 - - - +
66B PRO* 3.9 10.8 - - + -
67B GLN 4.5 0.2 - - - +
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Residues in contact with THR 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B ALA* 1.3 72.1 - - - +
25B VAL* 1.3 62.7 + - - +
26B PHE* 3.6 35.9 + - + -
32B GLN* 4.3 23.3 - - + +
33B LEU 3.5 8.3 - - - +
34B ARG* 4.2 17.4 + - + +
63B THR 3.7 0.3 - - - +
64B PHE* 4.0 0.3 - - - -
65B SER* 2.7 38.8 + - - -
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Residues in contact with VAL 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B ALA* 4.4 8.1 - - + +
24B THR* 1.3 70.6 - - - +
26B PHE* 1.3 63.1 + - - +
27B LEU* 3.6 10.6 + - + -
32B GLN* 3.3 3.4 - - - -
33B LEU* 2.5 47.0 + - + +
35B GLY 5.5 0.4 - - - +
47B LEU* 3.6 32.1 - - + -
56B VAL* 5.2 1.3 - - + -
61B ILE* 3.8 40.6 - - + -
63B THR 3.8 3.8 - - - +
64B PHE* 3.6 26.5 - - + -
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Residues in contact with PHE 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B THR* 3.7 29.8 - - + -
25B VAL* 1.3 71.6 - - - +
27B LEU* 1.3 58.5 + - - +
30B GLY 5.5 3.8 - - - -
31B PHE 4.0 2.7 - - - -
32B GLN* 3.5 26.9 - - + +
61B ILE* 3.6 2.8 - - - +
62B SER* 2.6 37.2 + - - +
63B THR* 3.1 35.8 + - + +
65B SER* 3.9 20.9 - - - -
1C MET 4.6 17.5 - - - -
2C LYS* 5.0 10.3 - - + -
29J ASN* 6.0 2.2 - - - +
31J PHE* 5.7 11.2 - + - -
54J GLN* 5.1 2.0 - - - -
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Residues in contact with LEU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A SER* 3.3 24.9 - - - +
63A THR* 4.1 2.0 - - - +
25B VAL* 4.2 11.2 - - + +
26B PHE* 1.3 81.8 - - - +
28B THR* 1.3 65.7 + - - +
29B ASN* 3.2 20.4 - - - +
30B GLY* 3.3 11.5 + - - -
31B PHE* 2.8 18.7 + - + +
33B LEU* 3.6 21.8 - - + -
56B VAL* 4.0 22.2 - - + -
60B ALA* 3.1 16.2 - - + +
61B ILE* 4.3 0.7 - - + -
62B SER* 4.0 5.7 - - - -
2F LYS* 3.6 26.2 - - - +
29J ASN* 4.3 5.7 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il